The genome sequence of the Scalloped Oak, Crocallis elinguaria (Linneas, 1758)

We present a genome assembly from an individual female Crocallis elinguaria (the Scalloped Oak; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 430.4 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,741 protein coding genes.


Background
Crocallis elinguaria (Scalloped Oak) is a macro-moth in the family Geometridae.The species is widespread and common throughout Britain and Europe, and occurs sporadically as far east as Siberia (GBIF Secretariat, 2023).The moth has undergone a large decline in abundance since the 1970s (Fox, 2013).Over the last 50 years, there has been a shift in its flight period, such that it now emerges earlier, with a peak occurrence in July rather than August (Randle et al., 2019).
The moth is found in a varied range of habitats, from woodlands to urban areas (Waring et al., 2017).At rest C. elinguaria holds its wings flat, appearing triangular in outline.The forewing edges are only slightly scalloped; the forewing length is 18-22 mm.The moth is very variable in colour, but the most common form is yellowish-buff with a darker brown central bar ornamented by a single black spot.There are forms which are orange-brown, dark brown or even blackish, with darker forms being more common in the north-west.C. elinguaria has one generation a year: it flies between July and August and regularly comes to light (Waring et al., 2017).The female lays her eggs on tree bark where they overwinter.The eggs hatch in early spring and the larvae are omnivorous, feeding on a wide range of woody plants (Leraut, 2009).
A genome sequence from C. elinguaria will be useful for research into colour variation in moths, and more generally for comparative studies across the Lepidoptera.The genome of C. elinguaria was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomally complete genome sequence for C. elinguaria based on the female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Crocallis elinguaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 44-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 103-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 10 missing joins or mis-joins, reducing the scaffold number by 29.41%. The final assembly has a total length of 430.4 Mb in 24 sequence scaffolds with a scaffold N50 of 28.5 Mb (Table 1).
A summary of the assembly statistics is shown in Figure 2, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.99%) of the assembly sequence was assigned to 17 chromosomal-level scaffolds, representing 15 autosomes and the Z and W sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/934829.

Sample acquisition and nucleic acid extraction
A female Crocallis elinguaria (specimen ID Ox000666, individual ilCroElin1) was collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.34) on 2020-07-20   using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilCroElin1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Abdomen tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Crocallis elinguaria assembly (GCA_907269065.1) in Ensembl Rapid Release.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject to the 'Darwin Tree of Life Project Sampling Code of Practice', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Table 3. Software tools: versions and sources.

Software tool Version
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.
The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Laurence Despres
Univ.Grenoble-Alpes, Grenoble, France In this data note, the authors report on the chromosome-level genome assembly of the Scalloped Oak, Crocallis elinguaria (Lepidoptera; Geometridae).a common and widely spread yet declining Eurasian wood moth.The assembly appears to be of good quality using appropriate methods : Pac Bio HiFi long reads (44-fold coverage), 10X genomics (103 fold-coverage) and Hi-C data to confirm scaffolding, manual curation of the final assembly, and following the high standard of the Darwin Tree of Life Project for results presentation.
The final assembly has a total length of 430.4 Mb and includes 17 chromosomes: 15 autosomes and the sexual Z and W chromosomes, as expected given that the specimen sequenced is a female.The mitogenome was also assembled.The quality of the assembly was further assessed by the proportion of complete BUSCO genes recovered, which is very high (>98% of Lepidoptera database BUSCO genes).Annotation was performed using BREAKER3 and 17,741 protein-coding genes were predicted.I have only one minor suggestion: Given the large range of colour variation described for this species you might highlight in the introduction that the specimen sequenced corresponds to the most common form by referring to the photo of the specimen presented in figure 1 at the end of this sentence: '... but the most common form is yellowish-buff with a darker brown central bar ornamented by a single black spot' (see figure 1).

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: population genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Crocallis elinguaria, ilCroElin1.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 430,399,360 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (38,734,590 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (28,485,152 and 17,265,692 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the lepidoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilCroElin1.1/dataset/CAJSMC01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Crocallis elinguaria, ilCroElin1.1:Hi-C contact map of the ilCroElin1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=fiJsohyJR0eJ6OJ1REeuiw.

©
2024 Thawornwattana Y.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Yuttapong Thawornwattana Harvard University, Cambridge, Massachusetts, USA Boyes & Boyes present a chromosomally complete assembly of Crocallis elinguaria (Linneas, 1758) (Lepidoptera: Geometridae), a moth collected from Wytham Woods, England.It was generated primarily PacBio HiFi, 10X and Hi-C data.The assembly is of high quality and will be useful to the research community.It contains 15 autosomes, the Z and W chromosomes and the mitochondrial genome.It is impressive to have the W chromosome in the assembly, but it is unclear in the Hi-C contact map (fig 5) which scaffold might corresponds to the W. Having chromosome labels in the figure would be useful.It would be nice to mention the expected haploid chromosome number, for example from cytology studies, to confirm that the chromosomes recovered here represent the complete genome.Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.Reviewer Expertise: evolutionary genomics, phylogenetics, insect evolution I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.Reviewer Report 03 April 2024 https://doi.org/10.21956/wellcomeopenres.22239.r76939© 2024 Despres L. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.